Welsh said he was flattered that the book, which celebrates its 20th anniversary this year, had even made it onto the list.
Lanark by Alasdair Gray was second, with Ian Rankin's Black and Blue third.
Responding to the poll, Welsh said: "I don't know if Trainspotting is the best Scottish book - I'm far from convinced it's my own best book.
"But I'm obviously flattered just to be on that list of great novels with those amazing writers, especially when I consider some of the brilliant books and my personal favourites that never made it onto this list."
Gray said he was "delighted and astonished" that his first novel, Lanark, had been judged more popular than a book by Rankin.
Black and Blue was Rankin's eighth Inspector Rebus tale.
The crime writer said it was an honour to be included in the top 10 with a book he regards "with great fondness".
He added: "I'm sure the results will be pored over and discussed, but what really matters is that books are still read with a passion. I feel sure this will be the case in another 50 years' time."
The 10 favourite Scottish novels of the last 50 years1. Trainspotting by Irvine Welsh (833 votes)
2. Lanark by Alasdair Gray (750)
3. Black and Blue by Ian Rankin (591)
4. The Bridge by Iain Banks (496)
5. One Fine Day in the Middle of the Night by Christopher Brookmyre (416)
6. Excession by Iain M Banks (330)
7. Morvern Callar by Alan Warner (296)
8. 44 Scotland Street by Alexander McCall Smith (282)
9. The Trick is to Keep Breathing by Janice Galloway (271)
10. Docherty by William McIlvanney (269)